Speaking Sunday at an Israeli Cabinet meeting, Netanyahu said: "Just in the last 36 hours the air force attacked Iranian warehouses containing Iranian weapons in the Damascus global airport".
Lt Col Jonathan Conricus said the final tunnel was the largest one discovered so far - running hundreds of metres from underneath a Lebanese home and deep into Israeli territory.
The IDF said the operation "removed the threat from the citizens of Israel".
With Israeli military forces announcing that Operation Northern Shield, which aimed at destroying alleged Hezbollah tunnels on the Israeli-Lebanese border, is coming to a close, the group along with Hamas has found another way of getting into the Jewish state-by using radio waves.
Israel is believed to have carried out hundreds of airstrikes against Iranian and Hezbollah targets throughout the Syrian civil war, but generally avoids commenting about them.
"According to our intelligence and our assessment of the situation there are no longer any cross-border attack tunnels from Lebanon into Israel". It said it holds the Lebanese government responsible for everything happening in its territory.
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Hezbollah has not commented on the tunnels, the existence of several of which was confirmed by United Nations peacekeepers in Lebanon.
Last month, Israel launched an operation to detect and destroy what was described as a vast network of Hezbollah tunnels, and officials say the latest discovery brings the mission to an end. It said the Iranian-backed organization Hezbollah dug the tunnels.
During his remarks to the cabinet, Netanyahu also thanked outgoing IDF chief Lt. Gen. Gadi Eisenkot for his service to the country. We will continue to monitor all activity by Hezbollah, and by Iran and its proxies.
Eisenkot told the New York Times: 'We struck thousands of targets without claiming responsibility or asking for credit'.
Israel has traditionally refrained from publicizing military operations against Iranian-linked targets on its northern front, but has been lifting the veil in recent days, a sign of confidence in a campaign waged amid occasional tension with Syria's big-power backer, Russia.
He pledged continued support for the Lebanese military and security forces and said that while Lebanon has the right to defend itself, "that is the right of the Lebanese state alone". "We yet have much work to do and we will do it", Netanyahu said.